[Chimera-users] Question about Model Loops Option in Chimera

[Elaine Meng]

Hi Ece (and others),
The bug in Chimera and ChimeraX, now fixed in both programs, was that when you choose "0" residues allowed to move, it was still allowing 1 residue on each side of the loop to move. To get the fix, download the current daily build:
<https://www.rbvi.ucsf.edu/chimera/download.html#daily>

In the fixed version, if you model loops and specify "0" residues adjacent to the loop allowed to move, then it will follow those instructions:  all the atoms except for the loops/segments you are modeling will stay exactly in the same place.

The protocol options (standard, DOPE, ...) are just which kind of scoring Modeller uses to choose the loop conformation, with DOPE being fancier/slower than the standard.  I think that is already mentioned in the Chimera help. It doesn't say much because I couldn't find much at the Modeller website, but I will try to make it better.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Dec 12, 2022, at 9:29 PM, Ben Webb via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> On 12/12/22 9:03 PM, Ecem Güngör via Chimera-users wrote:
>> What I found on the Modeller website is that potentially all of the atoms in the final model could move since either AutoLoop or LoopModel will try to build a comparative model using the input PDB as a template. You can check this site <https://salilab.org/modeller/wiki/Missing_residues>for more.
> 
> You are misinterpreting that text. Comparative modeling (which is what is described at that URL) will optimize the entire model by default (although you can ask it not to). Loop modeling of a given input structure will only move the loop atoms:
> https://salilab.org/modeller/10.4/manual/node36.html
> Of course, if you do comparative modeling followed by loop refinement, all the atoms will move because of the comparative modeling step.
> 
> (I had thought my answer when you asked about this a week ago on the Modeller mailing list addressed your question, but if anything wasn't clear, please let me know.)
> 
> 	Ben
> -- 
> ben at salilab.org                      https://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle
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